Announcing the Program namd

William F. Humphrey billh at lisboa.ks.uiuc.edu
Mon Jul 3 16:13:14 EST 1995


                     Announcing the Program namd
                     ---------------------------
The Theoretical Biophysics group at the University of Illinois and the
Beckman Institute would like to announce the availability the program namd, 
a new package for high performance parallel molecular dynamics simulations.
This software is being made available to the structural biology research 
community free of charge, and includes the source code for namd, documentation, 
and precompiled binaries for various parallel platforms The documentation, 
in postscript form, includes a programmers guide and a users guide.

Obtaining namd
-------------
A more complete description of namd is available via the namd WWW home page:
        http://www.ks.uiuc.edu:1250/Research/namd/

The software itself is available via anonymous ftp in the directory:
        ftp://ftp.ks.uiuc.edu/pub/mdscope/namd

Features
--------
namd is a molecular dynamics program designed to provide high performance 
simulations for large biological molecular systems.  Specifically, namd 
achieves high performance by exploiting the power of parallel computers 
and by providing a modular design that facilitates the implementation 
of new algorithms.  A high degree of modularity is obtained by using an 
object-oriented design and implementation in C++. namd uses spatial 
decomposition coupled with a multithreaded, message-driven design, which 
provides a scalable, efficient parallel framework.  namd also incorporates 
the Distributed Parallel Multipole Tree Algorithm (DPMTA) developed by the 
Scientific Computing group at Duke University, which allows full electrostatic 
force evaluation in O(N) time.  As part of the MDScope system, namd 
is connected via the communication system MDComm to the molecular graphics 
program VMD (also developed by the Theoretical Biophysics group) to provide 
such an interactive system where researchers can view and interact with a 
running simulation.

The program has many features, which include:
	o Input and output file compatibility with X-PLOR
	o CHARMM19 and CHARMM22 parameter support
	o Support for traditional MD functions such as energy minimization,
	  velocity rescaling, harmonic boundary conditions, harmonic
	  atom restraints, etc.
	o Full electrostatic evaluation using DPMTA from Duke University
	  integrated using a multiple timestep integration scheme.  For
	  more information on DPMTA, see the Scientific Computing home
	  page at:

		http://www.ee.duke.edu/Research/SciComp.html

	o Spatial decomposition for O(N/P) scalability of memory, computation,
	  and communication.
	o Message-driven, multithread design for high performance parallel
	  execution.
        o Modular, extensible source code using an object-oriented design in
          C++, with a programmers guide describing the source code structure.
	o Portable parallelism provided by PVM and Charm++ communication 
	  systems
        o Integration with the program VMD, a molecular graphics
	  program developed in the Theoretical Biophysics Group
	  at the University of Illinois.
          See the VMD WWW home page for more info:  

                  http://www.ks.uiuc.edu:1250/Research/vmd

          VMD can be used to set up and concurrently display a MD simulation
          using NAMD.  The two programs, along with the intermediary
          communications package (called MDComm) constitute the 'MDScope'
          environment.  


Availability
------------
namd should run on any parallel platform with a C++ compiler and PVM
version 3.3.6 or later.  Tested Makefiles are included for clusters
of HP, SGI, and IBM workstations, Cray T3D, and Convex Exemplar.
Precompiled binaries are provided for HP and SGI workstations.

VMD, NAMD, and the entire MDScope environment are part of an ongoing project
within the Theoretical Biophysics group to help provide free, effective tools
for molecular dynamics studies in structural biology.  This project is funded
by the National Institutes of Health and the National Science Foundation.



--
/*     		Bill Humphrey (billh at ks.uiuc.edu)		*/
/* Theoretical Biophysics		| Nothing matters but	*/
/* University of Illinois		| the weekend, from a	*/
/* 3117 Beckman Institute	 _______| Tuesday point of view	*/
/* 405 North Matthews		| phone: (217) 244-1851 	*/
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